Microsoft PowerPoint - Salisbury-richard_ ppt [Read-Only]

Size: px

Start display at page:

Download "Microsoft PowerPoint - Salisbury-richard_ ppt [Read-Only]"

ゆみかながだき
5 years ago
Views:

1 Genotyping with the Tag-It Mutation Detection Platform Richard Janeczko, PhD Salisbury, July 2004

2 MADRID TALK How to take penalty kicks

3 Overview The Tag-It Genotyping * Platform Tag-It Product Menu Cystic fibrosis, Ashkenazi Jewish Thrombophilia Drug metabolism (2D6, 2C9, 2C19) In Development Fragile X Infectious Disease (MRSA, viral genotypes)

4 Tag-It Product Specifications Accurate, robust, reproducible Flexible open system allows for Easy addition and subtraction of specific mutations by testing lab Open home-brew platform Variable sample throughput capability Software: Reports both wild-type and mutant alleles Integrates with LIMS and generates clinical reports Cost-effective

5 ASPE Genotyping with Tag-It or how to use the Tag-It Array Wild-type Mutant 3 3 A PCR-amplified DNA 3 T G 3 C 3 A T Denature Anneal allele-specific tagged primers Tag 1 Tag 2 T 3 3 G C C 3 Extend with DNA polymerase and biotin-dctp B 3 Tag 1 A T B Tag 2 3 G C B

6 Tag-It platform: product format HET WT target nucleic acid sample multiplex PCR multiplex ASPE hybridization detection on xmap reporting

7 Tag-It, Universal Array Sorting B SA PE Bead 1 Anti-Tag 1 B SA PE Bead 2 Anti-Tag 2 86 Luminex Bead Populations

8 Tag-It Cystic Fibrosis Products: Mutation Panels CFTR 23+4 (available March 5 th 2004) CFTR most prevalent (ACMG set)+ 4 reflex tests, Q CFTR 40+4 set ACMG set + 15 world s most common + 4 reflex tests, Q CFTR 71+4 CFTR 40+4 set + 31 expanded US and European coverage (in development), Q4 2004

9 Lab Requirements 4 Major Steps Schematic Hands On Time Genomic DNA (25 ng) I Multiplex PCR SAP-EXO Treatment 1 hr 5 µl of Treated PCR Reaction II Multiplex ASPE 15 min 5 µl of ASPE Reaction III Bead Hybridization 45 min Filtration and Wash IV Data Acquisition on xmap Data Analysis 5 min

10 Tag-It Multiplex (16-plex) PCR 500 bp 400 bp Ladder Ladder 300 bp 250 bp 271 bp amplimer 200 bp 175 bp Sample: Neg

11 net MFI ΔF508/ΔF508 CFTR 40+4: Net Signals (MFI) 0 G85E 394delTT R117H Y122X I148T 621+1G->T 711+1G->T 1078delT R334W R347 H/P A455E di507/df508 V520F w t mut/var 1 mut/var 2 var G->A G542X S549N S549R(T>G) G551D R553X A559T R560T mutation G->A G->T 2183/ insA G->A G->A Y1092X M1101K R1162X 3659delC S1255X(19) S1255X(20) kb 3876delA 3905insT W1282X N1303K 5/7/9 T var I506V/I507V/F508C net MFI ΔF508/R553X 0 G85E 394delTT R117H Y122X I148T 621+1G->T 711+1G->T 1078delT R334W R347 H/P A455E di507/df508 V520F w t mut/var 1 mut/var 2 var G->A G542X S549N S549R(T>G) G551D R553X A559T R560T mutation G->A G->T 2183/ insA G->A G->A Y1092X M1101K R1162X 3659delC S1255X(19) S1255X(20) kb 3876delA 3905insT W1282X N1303K 5/7/9 T var I506V/I507V/F508C

12 CFTR 40+4: Allelic Ratios mut AR ΔF508/ΔF G85E 394delTT R117H Y122X I148T 621+1G->T 711+1G->T 1078delT R334W R347 H/P A455E I507/508 V520F w t mut/var 1 mut/var 2 var G->A G542X S549N S549R(T>G) G551D R553X A559T R560T mutation G->A G->T 2183/ insA G->A G->A Y1092X M1101K R1162X 3659delC S1255X(19) S1255X(20) kb 3876delA 3905insT W1282X N1303K 5/7/9 T var I506V/I507V/F508C mut AR ΔF508/R553X 0.00 G85E 394delTT R117H Y122X I148T 621+1G->T 711+1G->T 1078delT R334W R347 H/P A455E I507/508 V520F w t mut/var 1 mut/var 2 var G->A G542X S549N S549R(T>G) G551D R553X A559T R560T mutation G->A G->T 2183/ insA G->A G->A Y1092X M1101K R1162X 3659delC S1255X(19) S1255X(20) kb 3876delA 3905insT W1282X N1303K 5/7/9 T var I506V/I507V/F508C

13 Tag-It Specificity df508 variation 1800 raw df508 signal WT HET (df508/wt) Mu D (df508) PCR neg raw wild-type signal

14 Correct Calls as a Function of S:N % called Tag-It Custom S:N ratio

15 Tag-It Data Acquisition Sample Description Median Fluorescence Intensity Bead Gate PCR Negative Bead Count

16 TDAS Summary View Genetic calls are displayed for each variation, for all samples.

17 Detailed Sample View All data and genetic calls are displayed for the selected sample.

18 Detailed Variation View All data and genetic calls are displayed for the selected variation.

19 Ashkenazi Jewish Panel Bloom Syndrome Canavan Disease Familial Dysautonomia Fanconi Anemia Group C Gaucher Disease Mucolipidosis Type IV (ML-IV) Niemann-Pick Disease Tay-Sachs disease

20 Additional Products PGx Panels (2D6, 2C9, 2C19) Fragile X Gene Dosage (aneuploidy) ID (MRSA, HPV)

21 Tag-It Advantage Multiplexed entire assay (86 alleles) tested in one well Complete genotyping analyzes both wildtype & mutant at each locus in each assay Accuracy S:N of 20:1 to 50:1 for each allele Automation Up to 1200 samples/day/technician in a 96-well format Menu CF40, Jewish panel (8 diseases), P450 testing (2D6, 2C9, 2C19), others

22 Tag-It Advantage No more reflexing reflex tests included in each assay, but results only shown if needed Full data analysis software provided; makes summary calls; can easily interface with LIS Low-cost instrument with ability to process 96 samples/40 minutes

IonTorrentPGM_appnote_0319.indd

IonTorrentPGM_appnote_0319.indd Ion PGM Heterogeneity * 1 * 1 * 2 * 2 * 2 * 2 * 2 * 1 *1 * 2 DNA DNA DNA ArcturusXT LCM Laser Capture Microdissection LCM A Workflow for Cancer Profiling Applied Biosystems ViiA7 PCR qpcr QC Assay Ion